Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 3CFV


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LYS 250 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225B  HIS*     3.4    16.8    +      -       -      -
    245B  VAL*     3.8     2.1    -      -       -      +
    246B  ALA      3.6    13.7    +      -       -      +
    248B  ASP*     2.9    44.4    +      -       +      +
    249B  GLN*     1.3    78.6    -      -       -      +
    251B  LEU*     1.3    59.0    +      -       -      +
    252B  MSE      3.9    18.4    -      -       +      -
    267B  LEU*     3.8    30.0    -      -       +      +
    268B  VAL      3.2    11.9    -      -       -      +
    269B  ASP*     3.4    29.7    +      -       -      +
    275B  VAL*     4.0     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  SER      3.6    15.3    -      -       -      +
    245B  VAL*     4.0    17.5    -      -       +      -
    250B  LYS*     1.3    71.6    -      -       -      +
    252B  MSE      1.3    69.6    +      -       -      +
    253B  ILE*     4.7     4.7    -      -       +      -
    266B  HIS      4.3     0.2    -      -       -      +
    267B  LEU*     3.8     0.3    -      -       -      -
    268B  VAL*     2.9    49.8    +      -       +      +
    270B  ALA*     3.9    16.6    -      -       +      +
    278B  LEU*     4.2    15.3    -      -       +      -
    288B  LEU*     4.3    17.5    -      -       +      -
    290B  THR*     4.2     5.6    -      -       -      +
    300B  TRP*     4.0    39.9    -      -       +      +
    305B  LEU*     4.9     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MSE 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  GLY      3.2    35.4    -      -       -      +
    225B  HIS*     3.6    32.1    -      -       +      +
    243B  GLY*     3.4     2.8    -      -       -      -
    244B  SER*     2.7    48.7    +      -       -      +
    248B  ASP*     3.8     9.0    -      -       -      +
    250B  LYS*     4.0    12.8    -      -       +      -
    251B  LEU*     1.3    79.0    -      -       -      +
    253B  ILE*     1.3    63.7    +      -       -      +
    254B  TRP*     3.7    16.2    -      -       -      +
    264B  PRO*     3.9    20.4    -      -       +      -
    266B  HIS      3.6     4.5    -      -       -      +
    267B  LEU*     3.9    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  LEU*     4.2    17.3    -      -       +      -
    242B  PHE      3.5     9.9    -      -       -      +
    243B  GLY*     4.6     7.9    -      -       -      -
    251B  LEU*     4.7    10.8    -      -       +      +
    252B  MSE      1.3    77.9    -      -       -      +
    254B  TRP*     1.3    70.6    +      -       -      +
    264B  PRO*     3.3     2.5    -      -       -      +
    265B  SER*     3.0    27.3    +      -       -      -
    266B  HIS*     3.2    30.7    +      -       +      -
    268B  VAL*     5.8     0.9    -      -       +      -
    280B  PHE*     5.4     3.8    -      -       +      -
    288B  LEU*     4.5    11.0    -      -       +      -
    302B  LEU*     3.3    35.7    -      -       +      -
    305B  LEU*     4.1    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 254 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  VAL*     5.9     1.7    -      -       +      +
    222B  PHE*     3.4    39.5    -      +       +      -
    224B  GLY*     3.3    40.6    -      -       -      -
    225B  HIS*     4.7     4.5    -      -       -      -
    240B  SER      4.4     0.2    -      -       -      -
    241B  LEU*     3.4    14.2    -      -       -      +
    242B  PHE*     2.8    71.5    +      +       +      -
    244B  SER*     2.6    28.1    +      -       -      -
    252B  MSE      3.7    19.3    -      -       -      +
    253B  ILE*     1.3    77.3    -      -       -      +
    255B  ASP*     1.3    61.7    +      -       -      +
    260B  THR      4.7     3.1    -      -       -      -
    261B  THR      4.2     0.2    -      -       -      -
    262B  SER      4.0     5.4    -      -       -      -
    263B  LYS      3.7    13.9    -      -       -      -
    264B  PRO*     3.7    34.5    -      -       +      -
    265B  SER*     4.5     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 255 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222B  PHE*     4.8     7.0    -      -       -      -
    240B  SER*     3.4     8.5    -      -       -      +
    241B  LEU*     4.1    12.2    -      -       +      +
    242B  PHE*     5.3     0.2    -      -       -      -
    254B  TRP*     1.3    78.3    -      -       -      +
    256B  THR*     1.3    75.6    +      -       -      +
    257B  ARG*     2.8    50.3    +      -       -      +
    258B  SER*     3.4    28.9    +      -       -      +
    260B  THR      5.5     1.4    -      -       -      +
    265B  SER*     3.7    19.0    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il